Complaints are like performance reviews: they tell you as much about the reviewer as the person being reviewed.
Recognising this, in a well run organisation, people will not be scared of making a justified complaint: they will think hard about whether the complaint is justified, but not about whether they should complain. Further, they will be confident that if their complaint is justified 'something will be done', and they will not suffer for coming forward.
Managers in such organisations will know their people well enough to be able to make value judgements about the people involved, and if they can't to find people who can. They will recognise genuine complaints that have merit, and will act on them.
I have a lot of people working for me. A few are serial complainers, recognised as such, and are periodically told to go away and grow up. Some will come with what they think is a serious issue, but I don't. I'll tell them why they are wrong, and expect them to respect my decision. (Sometimes, I will be wrong, but that's life.) Every now and again someone will come and tell me something that I need to know, and could not have identified for myself. Almost always, I will hear it from several places at once. Occasionally, I'll have to be patient, or find a way to verify it for myself. No-one is going to get crucified on one persons whim. But for the overall health of the organisation individuals who are underperforming need to be identified, and the company (and public) needs to be protected from them. Sometimes (alcoholics) they need to be protected from themselves.
Once the door of the cockpit closes there is very little a management can do to check on what goes on. One of the depressing things about Pprune, particularly in the context of something as important as flying commercial aircraft, is that it seems that pilots are prepared to fly with conspicuous underachievers, or people with serious personal problems, and do nothing about it. Is this because airline managments are all serially bad, or out of a misplaced sense of loyalty to the pilot community?
If Emirates are half the airline people claim, and the incidents were as trivial as people are saying, the captain should know he has nothing to fear. The F/O should have been told to grow up, in terms appropriate to the nature of his problem, and might have learnt one of life's lessons. Pilots in the bar, sipping iced tea, (as I'm sure they always do), would have commented 'silly sod', (if they ever heard about it) and left it at that.
And 411A would have had nothing to comment on. Utopia at last!